Oussama Assaidi was not even born the last time Stoke defeated Chelsea in the league but his sensational winner was enough to leave Jose Mourinho admitting “we are in trouble”.

Assaidi settled an absorbing encounter with a wonderful strike in the final minute as Mourinho was left to reflect on the profligacy of the forwards he has inherited and an opportunity wasted to close the gap on leaders Arsenal.

Mourinho trudged out of the Potteries with the look of a man on the brink of a mini-crisis and his response when asked how he can get his strikers to start scoring – “I don’t know” – suggested a much greater problem could be on the horizon.

Chelsea should have been out of sight by half-time but have now conceded six goals in two games and could be seven points behind Arsenal if Arsène Wenger’s team defeat Everton on Sunday.

They had appeared on course for their ninth win in the past 11 games against Stoke after Andre Schurrle’s early goal, in a first half Chelsea dominated, but the home team responded with a resilient performance that was a throwback to the gritty days of their early years in the Premier League under Tony Pulis.

And just when Stoke appeared content for a deserved point, Assaidi, signed on loan from Liverpool, cut inside to beat Petr Cech and condemn Mourinho to his third league defeat of the season. John Terry will not look back fondly on his 33rd birthday.

Mourinho was at a loss to explain what he had seen. “You don’t want me to criticise my player’s mistakes. I can’t. You can,” he said. “The problem is we didn’t score goals and we conceded goals, that was the mistake. After half an hour we should have been winning by three or four.

“We were playing so well, it was so easy and you find spaces, creating so much, you have to kill the game.

“But we are playing well. To be where we are, and you see us in relation to Arsenal, Manchester City, Manchester United, Tottenham and Liverpool, we are not doing badly even in term of points in the league.

“But we are not a physical team, we are not a team who can defend against physical teams. We need to score goals.”

The last time Stoke defeated them in the league was 1975 when Mud were No 1 with Oh Boy. There have been chastening defeats along the way, and Stoke might have feared another one when they fell behind after 10 minutes. An avalanche of Chelsea goals looked possible then.

It had seemed that there was nothing on as Schurrle received the ball from John Obi Mikel 30 yards out but the German international easily bypassed Ryan Shawcross, twice, before arrowing a low shot across Asmir Begovic into the bottom corner.

Schurrle’s goal, his second for Chelsea, set the tone for the half as his side took control. Eden Hazard, so inspired against Sunderland on Wednesday night, produced another menacing performance, constantly finding space as he tiptoed his way through Stoke’s midfield.

Chelsea had chances to increase their lead, with Juan Mata shooting straight at Begovic before Ramires lofted the ball over the crossbar.

“You’re going down with United” chanted the Chelsea fans, yet Mourinho clearly seemed perturbed at only being a goal ahead, frequently displaying his repertoire of extravagant gestures.

His anxiety proved well-founded. Stoke, who lost Charlie Adam through injury in the early stages, had offered little but equalised three minutes before half-time. Marko Arnautovic’s corner was not cleared and Crouch reacted quickest to turn and shoot under Petr Cech.

While that goal was scruffy, Stoke’s second was exquisite, six minutes into the second half. Jon Walters advanced down the right and sent Stephen Ireland clear. The midfielder curled a wonderful shot into the far corner.

Their lead lasted barely two minutes, however. Mata’s free-kick ricocheted off Crouch in the area and Schurrle’s half-volley gave Begovic no chance. Schurrle almost had a hat-trick, bending a shot that struck the top of the bar, before being substituted for Samuel Eto’o with an injury.

It was now a riveting game and Ireland wasted a decent chance before Frank Lampard, a substitute, failed to trouble Begovic with a free-kick.

Assaidi then produced a moment of magic to secure Mark Hughes only his second league win since August and it was no less than his side deserved.

The manager said: “It’s a great result for us and I thought it was a fantastic game but I would say that. We need a bit of credibility because we are trying to change things.

“There will be days when we are not particularly good with what we’re trying to do, but we have set our standards today and we have to maintain that.”